+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1mf8 | ||||||
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タイトル | Crystal Structure of human calcineurin complexed with cyclosporin A and human cyclophilin | ||||||
要素 |
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キーワード | HYDROLASE/ISOMERASE/IMMUNOSUPPRESSANT / HYDROLASE-ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CALCINEURIN-CYCLOPHILIN-CYCLOSPORIN COMPLEX / CYCLOSPORIN A (シクロスポリン) / IMMUNOSUPPRESSANT (免疫抑制剤) / HYDROLASE (加水分解酵素) / ISOMERASE (異性化酵素) | ||||||
機能・相同性 | 機能・相同性情報 negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / calcium-dependent protein serine/threonine phosphatase regulator activity / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / calcium-dependent protein serine/threonine phosphatase activity / protein serine/threonine phosphatase complex / negative regulation of signaling / positive regulation of saliva secretion / positive regulation of cardiac muscle hypertrophy in response to stress ...negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / calcium-dependent protein serine/threonine phosphatase regulator activity / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / calcium-dependent protein serine/threonine phosphatase activity / protein serine/threonine phosphatase complex / negative regulation of signaling / positive regulation of saliva secretion / positive regulation of cardiac muscle hypertrophy in response to stress / positive regulation of calcium ion import across plasma membrane / calmodulin-dependent protein phosphatase activity / slit diaphragm / calcineurin complex / positive regulation of connective tissue replacement / negative regulation of dendrite morphogenesis / calcineurin-mediated signaling / peptidyl-serine dephosphorylation / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / renal filtration / skeletal muscle tissue regeneration / regulation of synaptic vesicle cycle / positive regulation of calcineurin-NFAT signaling cascade / myelination in peripheral nervous system / transition between fast and slow fiber / negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / cardiac muscle hypertrophy in response to stress / positive regulation of osteoclast differentiation / regulation of postsynaptic neurotransmitter receptor internalization / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / parallel fiber to Purkinje cell synapse / virion binding / dendrite morphogenesis / Basigin interactions / cyclosporin A binding / myosin phosphatase activity / branching involved in blood vessel morphogenesis / protein serine/threonine phosphatase activity / CLEC7A (Dectin-1) induces NFAT activation / extrinsic component of plasma membrane / postsynaptic modulation of chemical synaptic transmission / protein-serine/threonine phosphatase / Minus-strand DNA synthesis / Plus-strand DNA synthesis / positive regulation of activated T cell proliferation / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / positive regulation of endocytosis / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Calcineurin activates NFAT / DARPP-32 events / positive regulation of cell adhesion / viral release from host cell / negative regulation of insulin secretion / Activation of BAD and translocation to mitochondria / 上皮間葉転換 / epidermis development / multicellular organismal response to stress / phosphatase binding / positive regulation of osteoblast differentiation / Binding and entry of HIV virion / positive regulation of viral genome replication / skeletal muscle fiber development / protein peptidyl-prolyl isomerization / 脱リン酸化 / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of protein dephosphorylation / keratinocyte differentiation / response to amphetamine / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / activation of protein kinase B activity / T細胞 / FCERI mediated Ca+2 mobilization / protein dephosphorylation / 好中球 / negative regulation of protein phosphorylation / プロリルイソメラーゼ / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / cellular response to glucose stimulus / G1/S transition of mitotic cell cycle / negative regulation of protein kinase activity / Assembly Of The HIV Virion / 筋鞘 / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / wound healing / Budding and maturation of HIV virion 類似検索 - 分子機能 | ||||||
生物種 | HOMO SAPIENS (ヒト) TOLYPOCLADIUM INFLATUM (菌類) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 3.1 Å | ||||||
データ登録者 | Jin, L. / Harrison, S.C. | ||||||
引用 | ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2002 タイトル: Crystal Structure of Human Calcineurin Complexed with Cyclosporin a and Human Cyclophilin 著者: Jin, L. / Harrison, S.C. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1mf8.cif.gz | 148.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1mf8.ent.gz | 120.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1mf8.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/mf/1mf8 ftp://data.pdbj.org/pub/pdb/validation_reports/mf/1mf8 | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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単位格子 |
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-要素
-タンパク質 , 3種, 3分子 ABC
#1: タンパク質 | 分子量: 42770.637 Da / 分子数: 1 / 断片: TRUNCATED FORM (RESIDUES 20-392) / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PETCN ALPHA / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) PLYSS 参照: UniProt: Q08209, protein-serine/threonine phosphatase |
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#2: タンパク質 | 分子量: 19322.904 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PETCN ALPHA / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) PLYSS 参照: UniProt: P63098, protein-serine/threonine phosphatase |
#3: タンパク質 | 分子量: 18036.504 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PET3A.CYPA / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) CODONPLUS RIL / 参照: UniProt: P62937, プロリルイソメラーゼ |
-タンパク質・ペプチド , 1種, 1分子 D
#4: タンパク質・ペプチド | |
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-非ポリマー , 2種, 5分子
#5: 化合物 | ChemComp-PO4 / |
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#6: 化合物 | ChemComp-CA / |
-詳細
構成要素の詳細 | CYCLOSPORI |
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-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.6 Å3/Da / 溶媒含有率: 46 % | ||||||||||||||||||||||||||||||||||||||||||
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結晶化 | pH: 4.6 詳細: 12% PEG 4000, 5MM POTASSIUM PHOSPHATE, 75MM SODIUM CITRATE, 15% GLYCEROL, 5MM TRIS, PH 4.6, MICROBATCH, TEMPERATURE 292K | ||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 19 ℃ / 手法: batch method | ||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: シンクロトロン / サイト: CHESS / ビームライン: F1 / 波長: 0.91611 |
検出器 | タイプ: ADSC QUANTUM 4 / 検出器: CCD / 日付: 2002年3月12日 |
放射 | モノクロメーター: SI 111 CHANNEL / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 0.91611 Å / 相対比: 1 |
反射 | 解像度: 3.1→15 Å / Num. obs: 14195 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / 冗長度: 5.3 % / Rsym value: 0.077 / Net I/σ(I): 19.3 |
反射 シェル | 解像度: 3.1→3.21 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.37 / % possible all: 81.7 |
反射 | *PLUS 最低解像度: 15 Å / Rmerge(I) obs: 0.077 |
反射 シェル | *PLUS 最高解像度: 3.1 Å / % possible obs: 81.7 % / Rmerge(I) obs: 0.377 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRY 1AUI AND 2RMA 解像度: 3.1→15 Å / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: ENGH & HUBER
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精密化ステップ | サイクル: LAST / 解像度: 3.1→15 Å
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拘束条件 |
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精密化 | *PLUS 最低解像度: 15 Å / Rfactor obs: 0.26 / Rfactor Rfree: 0.3 / Rfactor Rwork: 0.255 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS タイプ: c_bond_d / Dev ideal: 0.01 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | *PLUS 最高解像度: 3.1 Å / 最低解像度: 3.21 Å / Rfactor Rfree: 0.45 / Rfactor Rwork: 0.409 |